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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-SUCCINYL-6-HYDROXY-2,4-CYCLOHEXADIENE 1-CARBOXYLIC ACID SYNTHASE/2-OXOGLUTARATE DECARBOXYLASE FROM LISTERIA MONOCYTOGENES STR. 4B F2365
 
Authors :  Y. Patskovsky, R. Toro, J. Freeman, S. Hu, J. M. Sauder, S. K. Burley, S. C. Almo, New York Structural Genomix Research Consortium (Nysgxrc), New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  08 Feb 10  (Deposition) - 31 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (1x)
Keywords :  Menaquinone Biosynthesis, Sephchc Synthase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomix Research Consortium, Nysgxrc, Magnesium, Manganese, Metal-Binding, Thiamine Pyrophosphate, Transferase, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, J. Freeman, S. Hu, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Sephchc Synthase From Listeria Monocytogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE- 1-CARBOXYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.2.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 1-568
    Gene: MEND, LMOF2365_1699, PRK07449
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 265669
    Strain: 4B F2365
    Synonym: SEPHCHC SYNTHASE, MENAQUINONE BIOSYNTHESIS PROTEIN MEND

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B
Biological Unit 3 (2x): AB
Biological Unit 4 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3LQ1)

(-) Sites  (0, 0)

(no "Site" information available for 3LQ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LQ1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:164 -Pro A:165
2Glu A:177 -Pro A:178
3Glu A:184 -Pro A:185
4Gln A:451 -Pro A:452
5Thr B:164 -Pro B:165
6Glu B:177 -Pro B:178
7Glu B:184 -Pro B:185
8Gln B:451 -Pro B:452

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3LQ1)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:513
 aligned with MEND_LISMF | Q71YZ2 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:554
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551    
           MEND_LISMF     2 TNHEQVLTDYLAAFIEELVQAGVKEAIISPGSRSTPLALMMAEHPILKIYVDVDERSAGFFALGLAKASKRPVVLLCTSGTAAANYFPAVAEANLSQIPLIVLTADRPHELRNVGAPQAMDQLHLYGSHVKDFTDMALPENSEEMLRYAKWHGSRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPFTATGKKHHHVHIYYTHEVLDDSSIQKMVTECTGKKGVFVVGPIDKKELEQPMVDLAKKLGWPILADPLSGLRSYGALDEVVIDQYDAFLKEAEIIDKLTPEVVIRFGSMPVSKPLKNWLEQLSDIRFYVVDPGAAWKDPIKAVTDMIHCDERFLLDIMQQNMPDDAKDAAWLNGWTSYNKVAREIVLAEMANTTILEEGKIVAELRRLLPDKAGLFIGNSMPIRDVDTYFSQIDKKIKMLANRGANGIDGVVSSALGASVVFQPMFLLIGDLSFYHDMNGLLMAKKYKMNLTIVIVNNDGGGIFSFLPQANEPKYFESLFGTSTELDFRFAAAFYDADYHEAKSVDELEEAIDKASYHKGLDIIEVK 555
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.............hhhhh.eeee......hhhhhhhhhhhhhhhhhhhhh.....eeeeee..............------------..eeeeehhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh..eee.hhhh..........ee.hhhhhh.hhhhhhhh...eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..----..hhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....eeeee.........hhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhh...eeeeee...-------------------------...hhhhhhhh..eeee..hhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lq1 A   2 TNHEQVLTDYLAAFIEELVQAGVKEAIISPGSRSTPLALMMAEHPILKIYVDVDERSAGFFALGLAKASKRPVVLLCTSGTAAANYFPAVAEANLSQIPLIVLTADRPHELRNVGAPQAMDQLHLYGSHVKDFTDMALPENSEEMLRYAKWHGSRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPF------------YYTHEVLDDSSIQKMVTECTGKKGVFVVGPIDKKELEQPMVDLAKKLGWPILADPLSGLRSYGALDEVVIDQYDAFLKEAEIIDKLTPEVVIRFGSMPVSKPLKNWLEQLSDIRFYVVDPGAAWKDPIKAVTDMIHCDERFLLDIMQQNMPDDAKDAAWLNGWTSYNKVAREIVLAEMAN----EEGKIVAELRRLLPDKAGLFIGNSMPIRDVDTYFSQIDKKIKMLANRGANGIDGVVSSALGASVVFQPMFLLIGDLSFYHDMNGLLMAKKYKMNLTIVIVNND-------------------------ELDFRFAAAFYDADYHEAKSVDELEEAIDKASYHKGLDIIEVK 555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      |  -       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371        |-   |   391       401       411       421       431       441       451       461       471       481     |   -         -         - |     521       531       541       551    
                                                                                                                                                                                                                    188          201                                                                                                                                                                                380  385                                                                                                   487                       513                                          


Chain B from PDB  Type:PROTEIN  Length:518
 aligned with MEND_LISMF | Q71YZ2 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:554
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551    
           MEND_LISMF     2 TNHEQVLTDYLAAFIEELVQAGVKEAIISPGSRSTPLALMMAEHPILKIYVDVDERSAGFFALGLAKASKRPVVLLCTSGTAAANYFPAVAEANLSQIPLIVLTADRPHELRNVGAPQAMDQLHLYGSHVKDFTDMALPENSEEMLRYAKWHGSRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPFTATGKKHHHVHIYYTHEVLDDSSIQKMVTECTGKKGVFVVGPIDKKELEQPMVDLAKKLGWPILADPLSGLRSYGALDEVVIDQYDAFLKEAEIIDKLTPEVVIRFGSMPVSKPLKNWLEQLSDIRFYVVDPGAAWKDPIKAVTDMIHCDERFLLDIMQQNMPDDAKDAAWLNGWTSYNKVAREIVLAEMANTTILEEGKIVAELRRLLPDKAGLFIGNSMPIRDVDTYFSQIDKKIKMLANRGANGIDGVVSSALGASVVFQPMFLLIGDLSFYHDMNGLLMAKKYKMNLTIVIVNNDGGGIFSFLPQANEPKYFESLFGTSTELDFRFAAAFYDADYHEAKSVDELEEAIDKASYHKGLDIIEVK 555
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------TPP_enzyme_N-3lq1B03 B:10-186                                                                                                                                                    ---           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-3lq1B01 B:415-554                                                                                                              - Pfam domains (1)
           Pfam domains (2) --------TPP_enzyme_N-3lq1B04 B:10-186                                                                                                                                                    ---           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_enzyme_C-3lq1B02 B:415-554                                                                                                              - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.............hhhhh.eeee......hhhhhhhhhhhhhhhhhhhhh.....eeeeee...............-----------..eeeeehhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh..eee...............ee.hhhhhh.hhhhhhhh...eeeee.....hhhhhhhhhhh...eeeee..............eee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.....eeeee.........hhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhh...eeeeee...-------------------------..hhhhhhhhh..eeeee.hhhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lq1 B   2 TNHEQVLTDYLAAFIEELVQAGVKEAIISPGSRSTPLALMMAEHPILKIYVDVDERSAGFFALGLAKASKRPVVLLCTSGTAAANYFPAVAEANLSQIPLIVLTADRPHELRNVGAPQAMDQLHLYGSHVKDFTDMALPENSEEMLRYAKWHGSRAVDIAMKTPRGPVHLNFPLREPLVPILEPSPFT-----------YYTHEVLDDSSIQKMVTECTGKKGVFVVGPIDKKELEQPMVDLAKKLGWPILADPLSGLRSYGALDEVVIDQYDAFLKEAEIIDKLTPEVVIRFGSMPVSKPLKNWLEQLSDIRFYVVDPGAAWKDPIKAVTDMIHCDERFLLDIMQQNMPDDAKDAAWLNGWTSYNKVAREIVLAEMANTTILEEGKIVAELRRLLPDKAGLFIGNSMPIRDVDTYFSQIDKKIKMLANRGANGIDGVVSSALGASVVFQPMFLLIGDLSFYHDMNGLLMAKKYKMNLTIVIVNND-------------------------ELDFRFAAAFYDADYHEAKSVDELEEAIDKASYHKGLDIIEVK 555
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       | -       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481     |   -         -         - |     521       531       541       551    
                                                                                                                                                                                                                     189         201                                                                                                                                                                                                                                                                                           487                       513
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LQ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQ1)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: THDP-binding (106)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MEND_LISMF | Q71YZ2)
molecular function
    GO:0070204    2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity    Catalysis of the reaction: 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

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  Cis Peptide Bonds
    Gln A:451 - Pro A:452   [ RasMol ]  
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    Glu A:177 - Pro A:178   [ RasMol ]  
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  3lq1
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  2.2.1.9
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